Category: Science

As a kid I was transfixed by the remote worlds illustrated in the Peabody Museum’s murals of prehistoric creatures, and learned the skill of getting lost in the Museum of Natural History. With the scientific developments in the decades since those exhibits, I continue to find a well-told natural history an awe-inspiring tale; the stories of evolution, population dynamics, continental drift and climate change play out with accidents, contingencies, and deep patterns.

Tim Flannery’s Eternal Frontier is a big picture ecological history of North America, from the demise of the dinosaurs til yesterday. From a basic following of science news, I’d heard the theory that dinosaur extinction was caused by an asteroid impact. The book assembles a wide swath of evidence to pull together the big picture of massive destruction – the impact caused fire that burned most of North America; probably even more deadly was the dispersal of debris into the atmosphere, disrupting photosynthesis for months, causing ecosystems depending on land plants and plankton to die off. The result was massive extinctions on land and ocean. The stratigraphic evidence around the world shows a layer of sediment containing iridium, an element characteristic of asteroid material. In what is now North Dakota, 80% of all species disappeared above the iridium layer. According the fossil record, more species survived in fresh water, where the ecosystem is more dependent on detritus, than on dry land or ocean, where the ecosystem depends on photosynthesizing plants and plankton.

Many more deciduous plant species survived than evergreens, because they can “shut down” in times of stress, and for ten million years after the impact, decidious trees dominated in areas where evergreens would be otherwise favored by the climate. The anomalies caused by the asteroid impact serve to illustrate the more typical, longer-term patterns in North American ecology.

One of the strengths of the book is the way that Flannery illustrates large-scale patterns that play out over deep evolutionary time. One such pattern is North America’s distinctive sensitivity to climate change. The continent is shaped like wedge shape, with mountain chains running north/south. This geography results in causing in dramatic seasonal changes in temperature during the year than in other parts of the world and also magnifies the effects of global change in temperature. During two periods of global cooling at 50 and 38 million years ago, the deep sea temperature fell 4-5 degrees Celsius overall, but fell by about 9 degrees Celsius on the gulf coast.

Another deep pattern Flannery illustrates is the characteristic constellations of species in ecosystems. The African Seregeti has several major species: elephant, buffalo, rhino, lion. A similar ecosystem in North America was populated by mastodons, and later gomphotheres. The rhino role was played by Aphelops and Teleoceras. The big cat role was played by nimravids, and later on “barbourofelis” (illustration by the amazing natural history illustrator Carl Buell, aka Olduvai George.)

After major disruptions, Flannery shows that the ecosystem tends to repopulate with creatures of similar size, playing similar roles. This leads Flannery to leads to a recommendation (that he has supported for many years in his native Australia as well) to re-introduce species of megafauna such as elephants and camels that are missing in today’s ecosystem.

Speaking of missing species, Flannery reviews the evidence and finds the case compelling that humans caused the extinction of megafauna – sabre toothed tigers, mammoths, camels, sloths that roamed North America before humans arrived 13,000 years ago. The pattern isn’t just found in North America – humans arrived 50,000 years ago in Australia, and 6000 years ago in Cuba, and the megafauna disappeared at the time the humans arrived. Flannery makes that case that the species that flowed into North America after the arrival of humans had behavior that enabled them to survive predation – buffalo lived in large protective herds, and wolves had evolved near humans in Eurasia and had evolutionary time to learn fear. These behaviors worked until humans upgraded from knives to guns.

One of Flannery’s strengths is bringing together the evidence to tell big stories and illustrate big patterns. Two of the biggest patterns Flannery discusses also seems to me to be the most problematic.

The question with which Flannery frames the book is which continent originates the most species. Continents – largely isolated large landmasses – are biologically meaningful units in which evolution proceeds largely in isolation, so; examining the relative direction of population flow reveals interesting patterns. This lens also reveals interesting factoids – squirrels, dogs and camels all originated in North America. I don’t know about you, but I always wondered about species that seemed common to North American and Europe – what originated where? This book answers those questions. In addition to the question about population flow, there is also a real “history of science” question – the early dominance of North American evidence in paleolontology appears to be be a historical accident of caused by early enthusiasm and progress in North America; when you assemble paleontological results from other parts of the world you get a more balanced picture. And yet, aside from the real scientific and social history issues, the book is also replete with metaphorical language speculating about which continent will prove to be the “winner” in the global contest for originating the most species. This competitive framing sounds a bit too suspiciously like human geopolitics for comfort; the continental competition narrative reads like the Olympic television coverage of paleontology.

An even more problematic thesis is that of the frontier. There is a scientific element to it, in that North America has historically drawn influxes of species from Eurasia when the Bering crossing was open, and from South America when migration was possible; North America is a “frontier” into which new species spill and spread. Flannery sees the history of the immigration and diffusion of human cultures into North America in modern times as an instance of the same pattern. But the economic circumstances that have driven human migration to North America seem very weakly analogous to the geographic patterns that drove animal migration; the weakness of the hypothesis can be seen by looking at migrations that have nothing to do with geographical access – African Americans travelling North for manufacturing jobs; workers fleeing the rust belt for other parts of North America when manufacturing jobs move south and overseas. The reasons people move have everything to do with with human culture and financial resources.

Flannery draws his picture of the frontier from Turner – a historian who drew a romantic picture of a rough-and-ready, independent settler whose mindset is shaped by geographical expansion. There have been strong historical critiques of Turner – I’m most familiar William Cronon from his course in the American West and his book on the history of Chicago. Cronon shows how the exploitation of timber, mineral, and other resources were always closely tied to urban cultures and urban financial structures. More than that, the myth of frontier was shaped very early by theater and advertising; that Romantic self-image was heavily colored by fiction. And Turner’s focus on the white, Anglo frontiersman reflects his bias -there were African-Americans, Mexicans, ethnic Europeans; women and men. Turner’s Frontier is an important cultural myth, but a much weaker base for scientific comparison.

As a cultural myth, the Frontier and the death of the Frontier is a compelling narrative to explain the relentless exploitation of natural resources and the terrifying awareness — much later than the crisscrossing of the continent by railroads and telegraphs — that natural resources are limited and humans have the power to destroy our own civilization by mis-utilizing resources. The connection to the the flows of animal populations based on climate and geology is most tenuous. It would be better if Flannery drew a distinction but he doesn’t; the book tries to draw a seamless analogy between the population flows into North America across millions of years, and the cultural mythologies of manifest destiny and environmental exploitation, but the seams show.

Despite the weakness of the title argument, I really liked the book. if you are already deeply familiar with the scientific literature and have been following the topics closely across recent decades, this book may not have much new for you. If you are generally interested in the topic but not as familiar with the details, the book is fascinating. It is a strong entry in a genre of environmental history that weaves together paper-level detail to an accessible big picture story that shows the larger patterns across deep time.

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Steven Johnson’s The Invention of Air is a short, entertaining intellectual history of Priestley, an enlightenment polymath and radical who left his mark in science, religion, and politics. Johnson’s book is part of a genre, from Neal Stephenson to a spate Franklin biographies expressing nostalgia for good old fashioned enlightenment values in the age of the Bush adminisration’s anti-scientific, paleo-religious, wannabe tyranny.
Interesting the connections that Johnson draws and implies. Johnson hails Priestly as the forebear of ecoscience, since he was the first to identify plants creating the essential substance for animals to live. Johnson also notes that Preistley was the financial ward of England’s early industrialists who build the industrial age on the energy of burning fossil fuel and the labor of workers in the mines and factories. The seeds of the sustainability critique were planted at the same time industrial pollution began.
The book sympathizes with Priestley’s enlightenment critique of religious orthodoxy & political tyranny and pursuit of science, and the way his rationalist enthusiasm connected them all. Rather than connecting with the left’s critique of industrial waste, pollution, and oppression, Johnson emphasizes Priestley’s irrepressable optimism. Even as a scapegoat in his country and a political exile, Priestley kept up his experiments, preaching and polemic.
Perhaps the lesson for us is that we can learn from enlightenment optimism, too. What’s the right balance between skepticism toward an ideology of progress which blinds us to booms and hidden costs, and optimism that lets us create new solutions?

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The evolutionary history of animal development is producing some thrilling science these days. Like Endless Forms Most Beautiful, by Sean Carroll, Your Inner Fish is written for a general audience by one of the pioneering scientists in the field.
Neil Shubin is a paleontologist and developmental biologist whose team discovered Tiktaalik, a Devonian fish that is evolving toward tetrapod. The stage of tetrapod evolution is intriguing on its own — the creature jointed fins with ends that bend and splay, and a neck, allowing it to do “pushups” in shallow water to catch prey or watch for predators.
Carroll has more in-depth information than Shubin about the core of evo devo, the evolution of the developmental program that builds creatures with bodies. Where Shubin’s book shines is exploring the deep evolutionary history of different parts of the body, such as teeth, eyes, ears, and the head. The developmental program for teeth, out of the interaction between layers of skin in the embryo, also generates hair, feathers, and breasts. The bones, cartilage, and nerves in the human jaw, ears, and throat, expanded from tissues that served as gills in fish; the straightforward nerve routes in fish became convoluted in mammals now that the location of the tissues has been rearranged.
One of the most interesting chapters in the book covered the evolution of the building materials of bodies: collagen, cartilage, bone, intercellular communication. One fascinating hypothesis in this section is that one of the key bodybuilding materials, collagen, requires a lot of oxygen to produce. Therefore, a key factor in the explosion of animals with bodies in the Cambrian era was a rapid rise in the amount of oxygen in the atmosphere.
To follow up on this idea, I’m now reading Oxygen, the Molecule that Made the World.

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In general, I strongly prefer reading about the science of evolution, rather than arguments defending evolution against its detractors. The beautiful, rich stories of the evolution of life, supported by interlocking evidence in fossils, rocks, and dna are more interesting than the meta-argument. I don’t run into too many creationists in my usual social circles.
Every once in a while, I bump into some creationism. During the long wait for a car repair the other day, I was reading the fascinating story of Oxygen, in which the rocks, air and climate of the earth have been intertwingled with the evolution of life. On the drive back, flipping the tuner in search of a news station I stumbled upon a “creation science” radio show.
The theory of the creationists on the show depended on an assumption of rapidly varying rates of radioactive decay. They couldn’t explain why decay rates would fluctuate, except that God is all-wise and all-powerful. Moreover, they explained, all of the rock layers on earth, which conventional science attributes to billions of years of geologic story, were actually caused by intense volcanic activity and sedimentary deposition during the Flood 5000 years ago. How did Noah survive on the ark, with all the earth’s volcanic and sedimentary rock erupting and flowing around him? Miracles, of course. God is all-powerful.
Science is somewhat harder but much more interesting when you can’t use miracles to patch up the gaps in your logic.
This does raise interesting questions about information and persuasion. Americans’ beliefs tend to divert from orthodox religion when their personal experience diverges from religious teaching. A majority of young people support gay rights, and in general, people are more likely to support gay rights when they know family members, friends or colleagues who are gay. Their emotional experience overrides religious arguments.
Similarly, according to a a new Pew study, a (narrow) majority of American Christians believe that non-Christian religions can also lead to salvation. When people encounter good people with varying religious beliefs, they conclude that it isn’t plausible that only fellow Christians will go to heaven.
Americans come to support gay right and religious pluralism, based on their personal life experiences. So what of evolution? A person isn’t going to meet an australopithecus on the way to the store, or have a feathered dinosaur as a pet. The beautiful and compelling ideas of evolutionary development depend on basic understanding of genetics and developmentary biology. The case for evolution is made of fact and reason, not personal everyday experience.
There is a disturbing sub-plot running between the lines in Oxygen. Much of the innovative geology and paleontology was done in pre-WWII Germany. Science, of course, came to a halt, when society was taken over by a political movement with demented beliefs. What sort of society can educate its citizens so that a majority supports science?

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Descending to Newark airport a few weeks ago, ribbons of street lights and twinkling cars make a glowing carpet. Is this future nostalgia? In the near future, will we be able to afford highways? Will we be able to afford airplanes?
Since Ezra Klein went on vacation and turned his blog over to Prof Goose of the Oil Drum, I’ve been reading some of the peak oil bloggers, and it seems like there’s something to worry about.
* there is one major variable in the world’s oil equation, the Saudi supply. Information about Saudi capacity is closely held, and the Saudis have every reason to lie.
* new extraction techniques get more oil out of the ground sooner, and the depletion curve is steeper after a field’s production peaksWorldchanging covers the opportunities for new technology and increased efficiency with some practical optimism. Things might get very different in the non-distant future.
Update: Just read this Washington Post discussion with an analyst who concludes from research that Saudi production has peaked already. Yikes!

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The author of “Endless Forms Most Beautiful” cited Life on a Young Planet as a source, and one of his favorite science books.
Harvard paleontologist Andrew Knoll weaves together geology and paleontology to tell the story of life before the Cambrian Explosion. “Life on a Young Planet” explores scientific mysteries that don’t yet have clear answers.
In the Proterozoic age, 600 to 800 million years ago, there are clear signs of life, with bacteria and algae with colonial living patterns similar to their descendents in tidal flats today. Rewind to 3.5 billion years ago, and there are much more cryptic signs of life that can’t be conclusively distinguished from non-living processes.
Fast forward to 540 million years ago, at the end of the Proterozoic era, and there is a profusion of Vendobiont animal forms, strange and unlike the predecessors of recognizable organisms that proliferated during the “Cambrian Explosion.” Scientists still don’t know how or whether these alien creatures are related to the generations that followed.
One of my favorite sub-plots of the book is the story of the co-evolution of life and the planet. Early in earth’s history, oxygen was scarce. Early bacteria metabolized methane, sulfates, and other chemicals. The proliferation of cyanobacteria helped create the oxygen-rich atmosphere that allowed large and complicated life forms to flourish. Here, also, scientists still have unanswered questions about how the earth’s atmosphere evolved.
The book is clearly written, without condescension or the purple prose that affects some scientists freed of the constraints of journal articles. One of the strengths of the book is the way Knoll explains how scientists figure out what they know — the dating methods, chemical analysis, comparisons with modern life forms, geological mapping, and other techniques used to piece together the stories of ancient life.
I really enjoyed this book — it left me with a sense of awe about how much scientists have learned about the evolution of life, and how much is still unknown.

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The basic genetic software that drives the development of organisms is very old, and is shared in common across the animal kingdom. The software is modular, with components that govern the development of eyes, limbs, and hearts. The genetic program that builds a multi-faceted fly eye is mostly the same as the program that builds a human eye.
Components are re-used to build different body parts — the module that makes fingers and toes is re-used to make the spots on a butterfly. The genes are the same; the component architecture is the same, and the detail of the program itself is different.
This is beautiful science — general laws holding together a vast number of seemingly unrelated facts. And it’s new science. Until recently biologists theorized that eyes and limbs had developed independently in different families of organisms. The basic discoveries were made about 20 years ago, and much of the detail has been added in the last decade.

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The Birth of the Mind, by Gary Marcus, tells a fascinating story discovered in recent years about how genes drive the development of the brain. The primary puzzle is how 30,000 genes enable the creation of billions of neurons and trillions of connections. The answer is that genes aren’t like a blueprint with each gene coding for a component. Instead, genes act like computer programs, with behavior that is switched on and modified based on developmental and contextual cues. Brain wiring isn’t complete at birth or in childhood. Learning consists of rewiring the brain across the human lifespan.

Marcus hypothesizes for further research that the difference betweeen humans and chimpanzees isn’t just brain size, it’s differences in the developmental program. The same components are re-used and extended — the “then” parts of the genetic conditionals — the proteins produced — are the same but the “if” sections are different — the conditions and sequence in which the proteins are produced.

One of the interesting areas of discovery how modules are repurposed. The FOXP2 gene has been discovered to play a role in human language capabilities; it’s also used in the heart, lungs, and other areas. Another gene, PAX6, which controls eye-building, also used for “development of the central nervous system and endocrine glands, and regulates a range of cellular processes, including proliferation, migration, adhesion and signalling.” (from this paper by Marcus on FOXP2).

The story Marcus tells is complementary to the science sections of The Symbolic Species: The Coevolution of Language and the Brain, which describes the developmental patterns of neural growth. In human brains, neurons get extend and infiltrate from motory, sensory, and emotional centers through to centers of reason and planning, extending vocal calls to speech, foraging instincts to ethnic cuisine, emotions to poetry, weddings and funerals.

Unlike the Symbolic Species and recent books by Steven Pinker, Gary Marcus’ mentor at MIT, this book doesn’t stray as far into unprovable speculation about human nature and the origins of consciousness and culture. Which is just as well — the science is fascinating with less speculation. It is quite a thrill to read about a body of scientific knowledge that is growing so rapidly.

Daniel Dennett’s Freedom Evolves is on the speculation side of the continuum. No surprise, since Dennett’s a philosopher. The book tries to show how evolution can give rise to free will.
The first part of the book is a defense of an old philosophical perspective called “compatibilism”, whereby human free will is compatible with a deterministic universe. Even though natural events are predetermined, humans can choose to avoid determined events. For example, I might be genetically nearsighted, but can choose to wear glasses. The logical failure case is the intersection of multiple agents that each have free will. Ghandi chose nonviolent tactics to oppose British colonial rule, Indians chose to follow Gandhi’s nonviolent approach, and the British agreed to concede.

Following the defense of compatibilism, Dennett cites game theory and evolutionary biology to explain how humans may have evolved tendencies to co-operate, to develop ethical norms and social judgement. Dennett’s discussion of ethics seems rather impoverished. The examples he gives are mostly about the use of prison as just punishment, rather than the less extreme ethical issues that pervade social life. When discussing “free will”, Dennett tries to zero in on the rare circumstance of pure free choice, rather than the common situations where ones choices are influenced by habits (which one has chosen at some earlier date).

Dennett is vehemently in opposition to traditional, religiously derived perspectives. The book is studded with barbs against unnamed opponents who are supposedly terrified of the liberating impact of Dennett’s evolutionarily derived secular philosophy.

Yet spiritual thinkers from various traditions have more nuanced and insightful discussions about the range of ethical behavior, from parent-child relationships, to social gossip, to business ethics, to more extreme cases of crime and punishment. It is commonplace in Jewish ethical writing, for example, to talk about choosing good companions, teachers and habits to foster good choices.

Like Steven Pinker, Dennett scornfully replaces traditional ethical thought with modern, science-justified speculations that don’t, however, seem particularly wise. It is possible that moral philosophy guided by evolutionary science will contribute wisdom about the human condition; but these writers haven’t done it.
The developing science of mind, shaped by research in genetics, developmental biology, psychology, computational modeling, and evolutionary analysis is generating fascinating results. So far, the science seems more compelling to me than the philosophical speculation surrounding it.

In an Edge interview, Gary Marcus talks about how his perspective on the “nature/culture” issue differs from his mentor, Steven Pinker.

Pinker allows less room for improving the human condition than I would. I don’t think we disagree a whole lot about the nature of the facts, but Pinker tends to put his emphasis on the ways in which the biology constrains us in one direction or another, and he puts less emphasis on ways in which learning can change those things. I would say that the ability to learn is actually one of the things that humans are really good at. One of our unique talents is an incredible facility for learning, an incredible flexibility in learning, that even some of our closest primate cousins don’t have. Our miraculous abilities to learn actually open up lots of possibilities, and by not stressing this, Pinker in his latest book paints a somewhat darker picture of human nature than I would.